Chapter

Software Tools and Algorithms for Biological Systems

Volume 696 of the series Advances in Experimental Medicine and Biology pp 3-15

Date:

A Technical Platform for Generating Reproducible Expression Data from Streptomyces coelicolor Batch Cultivations

  • F. Battke
  • , A. Herbig
  • , A. Wentzel
  • , Ø. M. Jakobsen
  • , M. Bonin
  • , D. A. Hodgson
  • , W. Wohlleben
  • , T. E. Ellingsen
  • , STREAM Consortium
    • , K. NieseltAffiliated withFaculty of Science, Center for Bioinformatics Tübingen, University of Tübingen Email author 

* Final gross prices may vary according to local VAT.

Get Access

Abstract

Streptomyces coelicolor, the model species of the genus Streptomyces, presents a complex life cycle of successive morphological and biochemical changes involving the formation of substrate and aerial mycelium, sporulation and the production of antibiotics. The switch from primary to secondary metabolism can be triggered by nutrient starvation and is of particular interest as some of the secondary metabolites produced by related Streptomycetes are commercially relevant. To understand these events on a molecular basis, a reliable technical platform encompassing reproducible fermentation as well as generation of coherent transcriptomic data is required. Here, we investigate the technical basis of a previous study as reported by Nieselt et al. (BMC Genomics 11:10, 2010) in more detail, based on the same samples and focusing on the validation of the custom-designed microarray as well as on the reproducibility of the data generated from biological replicates. We show that the protocols developed result in highly coherent transcriptomic measurements. Furthermore, we use the data to predict chromosomal gene clusters, extending previously known clusters as well as predicting interesting new clusters with consistent functional annotations.

Keywords

Batch fermentation Chromosomal gene clusters Microarray design Streptomyces coelicolor